Pattern Identification in Biogeography

Author

Ganapathy, Ganeshkumar ; Goodson, Barbara ; Jansen, Robert ; Le, Hai-Son ; Ramachandran, Vijaya ; Warnow, Tandy

Author_Institution

Dept. of Comput. Sci., Texas Univ., Austin, TX

Volume

3

Issue

4

fYear

2006

Firstpage

334

Lastpage

346

Abstract

Identifying common patterns among area cladograms that arise in historical biogeography is an important tool for biogeographical inference. We develop the first rigorous formalization of these pattern-identification problems. We develop metrics to compare area cladograms. We define the maximum agreement area cladogram (MAAC) and we develop efficient algorithms for finding the MAAC of two area cladograms, while showing that it is NP-hard to find the MAAC of several binary area cladograms. We also describe a linear-time algorithm to identify if two area cladograms are identical

Keywords

biology computing; geography; optimisation; NP-hard problem; area cladograms; biogeography; linear-time algorithm; maximum agreement area cladogram; pattern identification; Biogeography; Bioinformatics; Computational biology; Geology; History; Inference algorithms; Organisms; Phylogeny; Stability; Tree data structures; Biogeography; area cladograms; distance metrics; maximum agreement area cladogram; maximum agreement subset.; Algorithms; Computer Simulation; Demography; Models, Genetic; Pattern Recognition, Automated; Phylogeny; Population Dynamics;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2006.57

Filename

4015376